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How do covalent intermediates help some enzymes catalyze reactions?

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A multi-panel diagram illustrates how a substrate binds to an enzyme's active site through induced fit, leading to product formation, and shows how non-substrates and allosteric regulators can alter enzyme activity by binding to different sites on the enzyme. — Enzyme In the induced-fit theory of enzyme-substrate binding, a substrate approaches the surface of an enzyme (step 1 in box A, B, C) and causes a change in the enzyme shape that results in the correct alignment of the catalytic groups (triangles A and B; circles C and D represent substrate-binding groups on the enzyme that are essential for catalytic activity). The catalytic groups react with the substrate to form products (step 2). The products then separate from the enzyme, freeing it to repeat the sequence (step 3). Boxes D and E represent examples of molecules that are too large or too small for proper catalytic alignment. Boxes F and G demonstrate binding of an inhibitor molecule (I and I′) to an allosteric site, thereby preventing interaction of the enzyme with the substrate. Box H illustrates binding of an allosteric activator (X), a nonsubstrate molecule capable of reacting with the enzyme.

In biochemistry, some enzymes catalyze reactions by forming a temporary covalent bond between the enzyme and a substrate, a process known as a double displacement reaction.1

This mechanism helps reactions proceed more rapidly by creating a covalent intermediate—an intermediate compound where a chemical bond exists between a specific group on the enzyme’s surface (such as an amino acid side chain) and a portion of the substrate.1

For example, in the action of acetylcholinesterase, a bond forms between the enzyme's serine residue and the acetyl group of the substrate. This creates an acetyl-enzyme complex, which then reacts with water to release the final product. Because the enzyme is regenerated at the end of the process, it remains a true catalyst despite being temporarily altered during the reaction. Various amino acids, including serine, cysteine, lysine, and glutamic acid, are commonly involved in forming these covalent linkages.1